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- PDB-7xbl: Dimeric structure of human galectin-7 in complex with three glycerol -

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Basic information

Entry
Database: PDB / ID: 7xbl
TitleDimeric structure of human galectin-7 in complex with three glycerol
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Promoting apoptosis Binding glycerol
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSi, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Int J Mol Sci / Year: 2022
Title: Binding of Glycerol to Human Galectin-7 Expands Stability and Modulates Its Functions.
Authors: Liang, Y. / Wang, Y. / Zhu, X. / Cai, J. / Shi, A. / Huang, J. / Zhu, Q. / Si, Y.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4705
Polymers30,1942
Non-polymers2763
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.851, 65.009, 73.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Galectin-7 / / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 15097.046 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli (E. coli) / References: UniProt: P47929
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes pH7.5, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2→20.93 Å / Num. obs: 17567 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.37 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 31.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.064 / Num. unique obs: 1255

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKZ

1bkz


Resolution: 2→20.93 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1753 10 %
Rwork0.1689 15775 -
obs0.1741 17528 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.71 Å2 / Biso mean: 22.9428 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 2→20.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 18 267 2393
Biso mean--25.97 30.61 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.19411300.15471169129998
2.05-2.110.23331320.158611881320100
2.11-2.180.26151330.164511991332100
2.18-2.260.24531320.16761190132299
2.26-2.350.2091330.174311981331100
2.35-2.450.22981340.17671198133299
2.45-2.580.23511340.18712161350100
2.58-2.750.24191330.195411961329100
2.75-2.960.25591360.192512251361100
2.96-3.250.22651360.17741216135299
3.25-3.720.20931350.15231216135199
3.72-4.680.18411400.150912591399100
4.68-20.930.23071450.1721305145099

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